> 1) What is the reason for the first 500ps of both plots for not being
> identical? Is it because the normalizing factors for the two
> auto-correlations being different?
Each point of a correlation function is an ensemble average over the whole
trajectory. The difference you get is due to the fact that you use
different structural ensembles (that partially overlap).
>
> 2) Could anyone please tell me the equation they use in amber to
> calculate
> the time-autocorrealtion functions?
There are several types of correlations functions one can compute. Show us
the ptraj command you used.
George
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Received on Wed May 22 2013 - 14:30:03 PDT
